DE analysis
gn <- as.character(ls_preprocessed$rna_all$Feature[which(ls_preprocessed$rna_all$Feature_gene_name =='PTGS2')])
DE_res <- DE_analysis(ls_preprocessed,
GeneBased=TRUE,
pDataBased=FALSE,
NewCondition=FALSE,
cond_nm= gn,
reference = 'low',
correct_gender=TRUE,
extremes_only=TRUE)
## Unlist done
## Labeling done
## Filtering done
## factor levels were dropped which had no samples
## Design done
## factor levels were dropped which had no samples
## Warning: Setting row names on a tibble is deprecated.
## vsd symbols done
## using pre-existing size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 1522 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
## DESeq done
## using 'normal' for LFC shrinkage, the Normal prior from Love et al (2014).
##
## Note that type='apeglm' and type='ashr' have shown to have less bias than type='normal'.
## See ?lfcShrink for more details on shrinkage type, and the DESeq2 vignette.
## Reference: https://doi.org/10.1093/bioinformatics/bty895
## res symbols done
## list done
DE results
heatmap_200(DE_res$res_df, DE_res$vsd_mat_sym, DE_res$meta_data, DE_res$pData_rnaseq)

x <- DE_res$res_df %>%
arrange(desc(abs(log2FoldChange)))
rownames(x) <- make.names(x$symbol, unique = T)
k <- gn
x <- x[-which(x$gene %in%k),]
#head(x, 10)
vp <- volcano_plot(x, gene=NULL, p_title='PTGS2', pCutoff=0.001, FCcutoff=1.5)

List of genes differentially expressed (-1.5 > fold change > 1.5, pval<0.001)
vp_tb <- vp$data[which(vp$data$Sig == 'FC_P'),]
rownames(vp_tb) <- c(1:nrow(vp_tb))
kable(vp_tb)
| 30.863992 |
-2.479060 |
0.3439049 |
-3.398115 |
0.0006785 |
0.0319640 |
ENSG00000088726.11 |
TMEM40 |
FC_P |
TMEM40 |
-2.479060 |
0.0006785 |
| 2964.903833 |
-2.207089 |
0.3797444 |
-5.472887 |
0.0000000 |
0.0001356 |
ENSG00000108602.13 |
ALDH3A1 |
FC_P |
ALDH3A1 |
-2.207089 |
0.0000000 |
| 15.439500 |
2.186333 |
0.3380666 |
6.398385 |
0.0000000 |
0.0000017 |
ENSG00000238939.1 |
snoU13 |
FC_P |
snoU13 |
2.186333 |
0.0000000 |
| 101.885165 |
-2.073900 |
0.3717441 |
-5.954557 |
0.0000000 |
0.0000144 |
ENSG00000227471.4 |
AKR1B15 |
FC_P |
AKR1B15 |
-2.073900 |
0.0000000 |
| 965.641295 |
2.048294 |
0.3423081 |
3.545670 |
0.0003916 |
0.0233105 |
ENSG00000130600.11 |
H19 |
FC_P |
H19 |
2.048294 |
0.0003916 |
| 705.858929 |
2.040664 |
0.3540554 |
5.952915 |
0.0000000 |
0.0000144 |
ENSG00000171246.5 |
NPTX1 |
FC_P |
NPTX1 |
2.040664 |
0.0000000 |
| 86.147620 |
-2.017125 |
0.3761486 |
-4.577180 |
0.0000047 |
0.0022361 |
ENSG00000196091.8 |
MYBPC1 |
FC_P |
MYBPC1 |
-2.017125 |
0.0000047 |
| 250.536264 |
1.972932 |
0.3800024 |
5.420838 |
0.0000001 |
0.0001387 |
ENSG00000144481.12 |
TRPM8 |
FC_P |
TRPM8 |
1.972932 |
0.0000001 |
| 18.120723 |
-1.971998 |
0.3771872 |
-5.205338 |
0.0000002 |
0.0002883 |
ENSG00000264785.1 |
RP11-311F12.2 |
FC_P |
RP11.311F12.2 |
-1.971998 |
0.0000002 |
| 221.303036 |
1.936225 |
0.3662064 |
6.089856 |
0.0000000 |
0.0000092 |
ENSG00000133055.4 |
MYBPH |
FC_P |
MYBPH |
1.936225 |
0.0000000 |
| 39.977179 |
1.919878 |
0.3578523 |
5.438106 |
0.0000001 |
0.0001356 |
ENSG00000163873.5 |
GRIK3 |
FC_P |
GRIK3 |
1.919878 |
0.0000001 |
| 47.209055 |
-1.900883 |
0.3664444 |
-5.286592 |
0.0000001 |
0.0002400 |
ENSG00000117971.7 |
CHRNB4 |
FC_P |
CHRNB4 |
-1.900883 |
0.0000001 |
| 34.643169 |
-1.889957 |
0.3497089 |
-5.368104 |
0.0000001 |
0.0001628 |
ENSG00000133454.11 |
MYO18B |
FC_P |
MYO18B |
-1.889957 |
0.0000001 |
| 88.440914 |
1.859034 |
0.3454515 |
5.116616 |
0.0000003 |
0.0003917 |
ENSG00000263293.1 |
RP11-290H9.4 |
FC_P |
RP11.290H9.4 |
1.859034 |
0.0000003 |
| 68.508056 |
-1.814031 |
0.3413006 |
-5.397081 |
0.0000001 |
0.0001478 |
ENSG00000230524.4 |
COL6A4P1 |
FC_P |
COL6A4P1 |
-1.814031 |
0.0000001 |
| 4.183238 |
-1.788793 |
0.3783275 |
-4.851113 |
0.0000012 |
NA |
ENSG00000259555.1 |
RP11-335K5.2 |
FC_P |
RP11.335K5.2 |
-1.788793 |
0.0000012 |
| 9.923174 |
-1.778642 |
0.3798210 |
-4.609164 |
0.0000040 |
0.0020054 |
ENSG00000266670.1 |
RN7SL637P |
FC_P |
RN7SL637P |
-1.778642 |
0.0000040 |
| 769.238937 |
1.763002 |
0.3354016 |
5.457343 |
0.0000000 |
0.0001356 |
ENSG00000136244.7 |
IL6 |
FC_P |
IL6 |
1.763002 |
0.0000000 |
| 35.220211 |
-1.760101 |
0.3744582 |
-4.675206 |
0.0000029 |
0.0018824 |
ENSG00000167419.6 |
LPO |
FC_P |
LPO |
-1.760101 |
0.0000029 |
| 127.247817 |
-1.758937 |
0.3760631 |
-4.797951 |
0.0000016 |
0.0013119 |
ENSG00000147573.12 |
TRIM55 |
FC_P |
TRIM55 |
-1.758937 |
0.0000016 |
| 76.308310 |
1.751477 |
0.3695326 |
4.938820 |
0.0000008 |
0.0007747 |
ENSG00000171864.4 |
PRND |
FC_P |
PRND |
1.751477 |
0.0000008 |
| 42.119413 |
-1.746615 |
0.3788470 |
-4.972110 |
0.0000007 |
0.0006994 |
ENSG00000204529.3 |
GUCY2EP |
FC_P |
GUCY2EP |
-1.746615 |
0.0000007 |
| 35.978596 |
1.736665 |
0.2768065 |
6.422754 |
0.0000000 |
0.0000017 |
ENSG00000273129.1 |
RP5-973M2.2 |
FC_P |
RP5.973M2.2 |
1.736665 |
0.0000000 |
| 812.764631 |
1.735449 |
0.3481507 |
4.104363 |
0.0000405 |
0.0072670 |
ENSG00000007908.11 |
SELE |
FC_P |
SELE |
1.735449 |
0.0000405 |
| 40.424738 |
-1.720007 |
0.3738841 |
-4.589461 |
0.0000044 |
0.0021395 |
ENSG00000237810.3 |
CTD-2571E19.3 |
FC_P |
CTD.2571E19.3 |
-1.720007 |
0.0000044 |
| 57.975367 |
1.691321 |
0.3594510 |
4.610884 |
0.0000040 |
0.0020054 |
ENSG00000054803.3 |
CBLN4 |
FC_P |
CBLN4 |
1.691321 |
0.0000040 |
| 386.091419 |
-1.676048 |
0.3762493 |
-4.431439 |
0.0000094 |
0.0032601 |
ENSG00000243955.1 |
GSTA1 |
FC_P |
GSTA1 |
-1.676048 |
0.0000094 |
| 304.948367 |
-1.652732 |
0.3606650 |
-4.416394 |
0.0000100 |
0.0033872 |
ENSG00000171658.4 |
RP11-443P15.2 |
FC_P |
RP11.443P15.2 |
-1.652732 |
0.0000100 |
| 10.844419 |
-1.643394 |
0.3800087 |
-4.372455 |
0.0000123 |
0.0036919 |
ENSG00000163793.8 |
DNAJC5G |
FC_P |
DNAJC5G |
-1.643394 |
0.0000123 |
| 261.716752 |
-1.613595 |
0.3376515 |
-4.733409 |
0.0000022 |
0.0015713 |
ENSG00000174564.8 |
IL20RB |
FC_P |
IL20RB |
-1.613595 |
0.0000022 |
| 21.962206 |
-1.609315 |
0.3619317 |
-4.487156 |
0.0000072 |
0.0028131 |
ENSG00000215644.5 |
GCGR |
FC_P |
GCGR |
-1.609315 |
0.0000072 |
| 30.302262 |
1.604662 |
0.2948598 |
5.533832 |
0.0000000 |
0.0001282 |
ENSG00000249545.1 |
CTC-558O19.1 |
FC_P |
CTC.558O19.1 |
1.604662 |
0.0000000 |
| 457.989439 |
-1.587791 |
0.3304879 |
-5.023543 |
0.0000005 |
0.0005727 |
ENSG00000113924.7 |
HGD |
FC_P |
HGD |
-1.587791 |
0.0000005 |
| 573.891976 |
-1.587627 |
0.3443689 |
-4.470575 |
0.0000078 |
0.0029355 |
ENSG00000160211.11 |
G6PD |
FC_P |
G6PD |
-1.587627 |
0.0000078 |
| 4420.543243 |
-1.580947 |
0.3697534 |
-4.115958 |
0.0000386 |
0.0070693 |
ENSG00000187134.8 |
AKR1C1 |
FC_P |
AKR1C1 |
-1.580947 |
0.0000386 |
| 9.824994 |
1.577737 |
0.3709120 |
4.392523 |
0.0000112 |
0.0035468 |
ENSG00000252431.1 |
RNU6-1247P |
FC_P |
RNU6.1247P |
1.577737 |
0.0000112 |
| 81.580956 |
1.575815 |
0.3665399 |
4.349913 |
0.0000136 |
0.0037911 |
ENSG00000141433.8 |
ADCYAP1 |
FC_P |
ADCYAP1 |
1.575815 |
0.0000136 |
| 40.121661 |
1.564765 |
0.3784804 |
4.211927 |
0.0000253 |
0.0054779 |
ENSG00000165606.4 |
DRGX |
FC_P |
DRGX |
1.564765 |
0.0000253 |
| 10.846014 |
-1.563250 |
0.3751473 |
-4.081284 |
0.0000448 |
0.0075193 |
ENSG00000149742.5 |
SLC22A9 |
FC_P |
SLC22A9 |
-1.563250 |
0.0000448 |
| 20.669399 |
-1.546334 |
0.3529611 |
-4.532112 |
0.0000058 |
0.0025835 |
ENSG00000253379.1 |
RP11-1102P16.1 |
FC_P |
RP11.1102P16.1 |
-1.546334 |
0.0000058 |
| 14.343559 |
-1.537542 |
0.3739281 |
-4.324996 |
0.0000153 |
0.0040386 |
ENSG00000233080.2 |
CTA-714B7.5 |
FC_P |
CTA.714B7.5 |
-1.537542 |
0.0000153 |
| 4843.472295 |
1.536494 |
0.3480689 |
4.948693 |
0.0000007 |
0.0007644 |
ENSG00000104368.13 |
PLAT |
FC_P |
PLAT |
1.536494 |
0.0000007 |
| 5.078966 |
-1.535966 |
0.3737345 |
-4.644839 |
0.0000034 |
0.0018824 |
ENSG00000258145.1 |
BX927168.3 |
FC_P |
BX927168.3 |
-1.535966 |
0.0000034 |
| 33.637824 |
1.534993 |
0.3606770 |
4.649579 |
0.0000033 |
0.0018824 |
ENSG00000270080.1 |
RP6-99M1.2 |
FC_P |
RP6.99M1.2 |
1.534993 |
0.0000033 |
| 6.026043 |
1.534644 |
0.3806103 |
3.953790 |
0.0000769 |
0.0101133 |
ENSG00000256870.2 |
SLC5A8 |
FC_P |
SLC5A8 |
1.534644 |
0.0000769 |
| 573.446918 |
1.528067 |
0.3223235 |
4.462010 |
0.0000081 |
0.0030206 |
ENSG00000259207.3 |
ITGB3 |
FC_P |
ITGB3 |
1.528067 |
0.0000081 |
| 132.344366 |
1.523856 |
0.3629211 |
4.155283 |
0.0000325 |
0.0063099 |
ENSG00000108342.8 |
CSF3 |
FC_P |
CSF3 |
1.523856 |
0.0000325 |
| 8.860518 |
-1.523608 |
0.3714336 |
-4.155370 |
0.0000325 |
0.0063099 |
ENSG00000261303.1 |
RP11-160C18.2 |
FC_P |
RP11.160C18.2 |
-1.523608 |
0.0000325 |
| 289.481825 |
-1.521638 |
0.3709542 |
-3.988755 |
0.0000664 |
0.0090801 |
ENSG00000249628.2 |
LINC00942 |
FC_P |
LINC00942 |
-1.521638 |
0.0000664 |
| 2.838738 |
-1.518618 |
0.3800038 |
-3.927524 |
0.0000858 |
NA |
ENSG00000221446.1 |
AC099805.1 |
FC_P |
AC099805.1 |
-1.518618 |
0.0000858 |
| 23.427723 |
-1.514773 |
0.3689689 |
-3.927944 |
0.0000857 |
0.0107002 |
ENSG00000219700.1 |
PTCHD3P3 |
FC_P |
PTCHD3P3 |
-1.514773 |
0.0000857 |
| 42.741613 |
1.514567 |
0.3694188 |
5.189432 |
0.0000002 |
0.0002883 |
ENSG00000252236.1 |
SNORA26 |
FC_P |
SNORA26 |
1.514567 |
0.0000002 |
| 21.315531 |
-1.514550 |
0.3790428 |
-3.840276 |
0.0001229 |
0.0126920 |
ENSG00000175329.8 |
ISX |
FC_P |
ISX |
-1.514550 |
0.0001229 |
| 1200.534861 |
1.513667 |
0.3714697 |
4.473439 |
0.0000077 |
0.0029301 |
ENSG00000196611.4 |
MMP1 |
FC_P |
MMP1 |
1.513667 |
0.0000077 |
| 4456.952479 |
1.513016 |
0.3026534 |
5.465515 |
0.0000000 |
0.0001356 |
ENSG00000119508.13 |
NR4A3 |
FC_P |
NR4A3 |
1.513016 |
0.0000000 |
| 1600.004739 |
-1.511491 |
0.2998332 |
-4.895326 |
0.0000010 |
0.0008455 |
ENSG00000159228.8 |
CBR1 |
FC_P |
CBR1 |
-1.511491 |
0.0000010 |
| 66.282187 |
-1.504971 |
0.3766435 |
-4.121835 |
0.0000376 |
0.0069794 |
ENSG00000254632.1 |
RP11-21L23.4 |
FC_P |
RP11.21L23.4 |
-1.504971 |
0.0000376 |
| 492.343147 |
-1.503084 |
0.3317930 |
-4.496096 |
0.0000069 |
0.0027300 |
ENSG00000181652.14 |
ATG9B |
FC_P |
ATG9B |
-1.503084 |
0.0000069 |
Pathway enrichment analysis fGSEA
Low PTGS2 is the reference. When PTGS2 is high, pathways shown below are up- or down- regulated
fgsea_res <- fgsea_analysis(DE_res)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
fgp <- fgsea_plot(fgsea_res$res_hm, pathways_title='Hallmark', condition_name='PTGS2 low vs high')

kable(fgp)
| HALLMARK_TNFA_SIGNALING_VIA_NFKB |
0.0028653 |
0.0062469 |
0.6718790 |
3.452653 |
0 |
195 |
up |
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION |
0.0028249 |
0.0062469 |
0.6070484 |
3.113228 |
0 |
189 |
up |
| HALLMARK_INFLAMMATORY_RESPONSE |
0.0028490 |
0.0062469 |
0.5254339 |
2.699209 |
0 |
193 |
up |
| HALLMARK_UV_RESPONSE_DN |
0.0027855 |
0.0062469 |
0.4620131 |
2.268724 |
0 |
136 |
up |
| HALLMARK_TGF_BETA_SIGNALING |
0.0025510 |
0.0062469 |
0.5363940 |
2.224683 |
0 |
54 |
up |
| HALLMARK_ANDROGEN_RESPONSE |
0.0026178 |
0.0062469 |
0.4704808 |
2.168803 |
0 |
96 |
up |
| HALLMARK_KRAS_SIGNALING_UP |
0.0028249 |
0.0062469 |
0.4210727 |
2.158492 |
0 |
190 |
up |
| HALLMARK_IL6_JAK_STAT3_SIGNALING |
0.0025907 |
0.0062469 |
0.4581458 |
2.052373 |
0 |
82 |
up |
| HALLMARK_ANGIOGENESIS |
0.0024272 |
0.0062469 |
0.5333233 |
2.010585 |
0 |
35 |
up |
| HALLMARK_APOPTOSIS |
0.0028249 |
0.0062469 |
0.4034059 |
2.005791 |
0 |
155 |
up |
| HALLMARK_IL2_STAT5_SIGNALING |
0.0028249 |
0.0062469 |
0.3818565 |
1.957463 |
0 |
190 |
up |
| HALLMARK_PROTEIN_SECRETION |
0.0025253 |
0.0062469 |
0.4154849 |
1.901594 |
0 |
89 |
up |
| HALLMARK_FATTY_ACID_METABOLISM |
0.0015625 |
0.0062469 |
-0.3946258 |
-1.811652 |
0 |
147 |
down |
| HALLMARK_HYPOXIA |
0.0028653 |
0.0062469 |
0.3520276 |
1.791540 |
0 |
180 |
up |
| HALLMARK_XENOBIOTIC_METABOLISM |
0.0015267 |
0.0062469 |
-0.3755563 |
-1.785475 |
0 |
188 |
down |
| HALLMARK_KRAS_SIGNALING_DN |
0.0015291 |
0.0062469 |
-0.3736344 |
-1.759588 |
0 |
179 |
down |
| HALLMARK_ALLOGRAFT_REJECTION |
0.0028736 |
0.0062469 |
0.3329580 |
1.699892 |
0 |
187 |
up |
| HALLMARK_GLYCOLYSIS |
0.0015267 |
0.0062469 |
-0.3449329 |
-1.639885 |
0 |
188 |
down |
| HALLMARK_MYC_TARGETS_V1 |
0.0028249 |
0.0062469 |
0.3121833 |
1.601022 |
0 |
189 |
up |
| HALLMARK_COMPLEMENT |
0.0028490 |
0.0062469 |
0.3115283 |
1.600353 |
0 |
193 |
up |
| HALLMARK_INTERFERON_ALPHA_RESPONSE |
0.0016077 |
0.0062469 |
-0.3704954 |
-1.583910 |
0 |
93 |
down |
| HALLMARK_COAGULATION |
0.0028329 |
0.0062469 |
0.3205127 |
1.544766 |
0 |
127 |
up |
| HALLMARK_INTERFERON_GAMMA_RESPONSE |
0.0028409 |
0.0062469 |
0.2858225 |
1.468669 |
0 |
194 |
up |
| HALLMARK_E2F_TARGETS |
0.0030864 |
0.0064300 |
-0.3057234 |
-1.455121 |
1 |
191 |
down |
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY |
0.0033333 |
0.0066667 |
-0.4506941 |
-1.677822 |
1 |
46 |
down |
| HALLMARK_CHOLESTEROL_HOMEOSTASIS |
0.0076531 |
0.0147174 |
0.3778151 |
1.637235 |
2 |
69 |
up |
| HALLMARK_DNA_REPAIR |
0.0185471 |
0.0343466 |
-0.2994121 |
-1.371389 |
11 |
141 |
down |
fgp <- fgsea_plot(fgsea_res$res_c1, pathways_title='C1 positional genes', condition_name='PTGS2 low vs high')

kable(fgp)
| chr14q22 |
0.0026385 |
0.0087704 |
0.6480918 |
2.718198 |
0 |
62 |
up |
| chr17q25 |
0.0014706 |
0.0087704 |
-0.5605161 |
-2.712166 |
0 |
202 |
down |
| chr14q11 |
0.0015038 |
0.0087704 |
-0.5576148 |
-2.677608 |
0 |
196 |
down |
| chr2q33 |
0.0025974 |
0.0087704 |
0.5664097 |
2.633529 |
0 |
103 |
up |
| chr3q12 |
0.0024096 |
0.0087704 |
0.7217473 |
2.613571 |
0 |
30 |
up |
| chr16p13 |
0.0014065 |
0.0087704 |
-0.5038103 |
-2.514918 |
0 |
272 |
down |
| chr5q22 |
0.0024450 |
0.0087704 |
0.6585974 |
2.507448 |
0 |
38 |
up |
| chr16p11 |
0.0016051 |
0.0087704 |
-0.5485333 |
-2.457501 |
0 |
120 |
down |
| chr5q11 |
0.0024814 |
0.0087704 |
0.6180480 |
2.444376 |
0 |
45 |
up |
| chr15q21 |
0.0025445 |
0.0087704 |
0.5242948 |
2.443386 |
0 |
102 |
up |
| chr13q14 |
0.0026667 |
0.0087704 |
0.4804116 |
2.398577 |
0 |
151 |
up |
| chr5p13 |
0.0026110 |
0.0087704 |
0.5180763 |
2.332600 |
0 |
84 |
up |
| chr8q24 |
0.0015060 |
0.0087704 |
-0.4854562 |
-2.314193 |
0 |
185 |
down |
| chr1p36 |
0.0013333 |
0.0087704 |
-0.4452136 |
-2.302088 |
0 |
395 |
down |
| chr13q22 |
0.0023202 |
0.0087704 |
0.6562163 |
2.293964 |
0 |
26 |
up |
| chr11q13 |
0.0013986 |
0.0087704 |
-0.4526367 |
-2.273656 |
0 |
290 |
down |
| chr13q32 |
0.0025445 |
0.0087704 |
0.5285869 |
2.269814 |
0 |
67 |
up |
| chr2q31 |
0.0025641 |
0.0087704 |
0.4906042 |
2.259812 |
0 |
94 |
up |
| chr9q33 |
0.0025974 |
0.0087704 |
0.4853644 |
2.253236 |
0 |
104 |
up |
| chr2p16 |
0.0024272 |
0.0087704 |
0.5483907 |
2.245510 |
0 |
51 |
up |
| chr1q44 |
0.0024691 |
0.0087704 |
0.5490340 |
2.202901 |
0 |
48 |
up |
| chr8p23 |
0.0026247 |
0.0087704 |
0.4896963 |
2.202366 |
0 |
83 |
up |
| chr2q32 |
0.0026042 |
0.0087704 |
0.5184409 |
2.183116 |
0 |
63 |
up |
| chr8p22 |
0.0023585 |
0.0087704 |
0.6335003 |
2.177043 |
0 |
25 |
up |
| chr18p11 |
0.0026110 |
0.0087704 |
0.4664890 |
2.143784 |
0 |
93 |
up |
| chr11q14 |
0.0025253 |
0.0087704 |
0.4835247 |
2.135441 |
0 |
76 |
up |
| chr3p14 |
0.0026247 |
0.0087704 |
0.4744171 |
2.133649 |
0 |
83 |
up |
| chr13q13 |
0.0024938 |
0.0087704 |
0.5372955 |
2.133397 |
0 |
46 |
up |
| chr12q21 |
0.0025445 |
0.0087704 |
0.4972314 |
2.126432 |
0 |
66 |
up |
| chr9p21 |
0.0024272 |
0.0087704 |
0.5187922 |
2.124312 |
0 |
51 |
up |
fgp <- fgsea_plot(fgsea_res$res_c2, pathways_title='C2 curated genes', condition_name='PTGS2 low vs high')

kable(fgp)
| PHONG_TNF_TARGETS_UP |
0.0024213 |
0.02415 |
0.7491497 |
3.144365 |
0 |
62 |
up |
| ANASTASSIOU_MULTICANCER_INVASIVENESS_SIGNATURE |
0.0024213 |
0.02415 |
0.7340077 |
3.080811 |
0 |
62 |
up |
| CHEN_HOXA5_TARGETS_9HR_UP |
0.0029326 |
0.02415 |
0.5944775 |
3.077183 |
0 |
211 |
up |
| BROCKE_APOPTOSIS_REVERSED_BY_IL6 |
0.0028090 |
0.02415 |
0.6128985 |
2.972529 |
0 |
140 |
up |
| PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_DN |
0.0028409 |
0.02415 |
0.6237117 |
2.953786 |
0 |
128 |
up |
| TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_UP |
0.0025000 |
0.02415 |
0.6959614 |
2.945391 |
0 |
66 |
up |
| UZONYI_RESPONSE_TO_LEUKOTRIENE_AND_THROMBIN |
0.0023474 |
0.02415 |
0.8018658 |
2.930540 |
0 |
34 |
up |
| KEGG_RIBOSOME |
0.0026810 |
0.02415 |
0.6687799 |
2.913266 |
0 |
81 |
up |
| REACTOME_RESPONSE_OF_EIF2AK4_GCN2_TO_AMINO_ACID_DEFICIENCY |
0.0026455 |
0.02415 |
0.6396325 |
2.893407 |
0 |
94 |
up |
| WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN |
0.0029412 |
0.02415 |
0.5684874 |
2.887739 |
0 |
184 |
up |
| PECE_MAMMARY_STEM_CELL_DN |
0.0028329 |
0.02415 |
0.6026885 |
2.870170 |
0 |
132 |
up |
| REACTOME_EUKARYOTIC_TRANSLATION_INITIATION |
0.0028011 |
0.02415 |
0.6114179 |
2.857685 |
0 |
112 |
up |
| VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_UP |
0.0029070 |
0.02415 |
0.5716292 |
2.848274 |
0 |
161 |
up |
| REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE |
0.0027322 |
0.02415 |
0.6205736 |
2.843983 |
0 |
104 |
up |
| REACTOME_EUKARYOTIC_TRANSLATION_ELONGATION |
0.0026596 |
0.02415 |
0.6409805 |
2.831947 |
0 |
86 |
up |
| LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN |
0.0028736 |
0.02415 |
0.5957315 |
2.829795 |
0 |
129 |
up |
| NAGASHIMA_NRG1_SIGNALING_UP |
0.0029940 |
0.02415 |
0.5604463 |
2.807712 |
0 |
167 |
up |
| NIKOLSKY_BREAST_CANCER_16P13_AMPLICON |
0.0015601 |
0.02415 |
-0.6373712 |
-2.795941 |
0 |
105 |
down |
| ZHENG_FOXP3_TARGETS_IN_THYMUS_UP |
0.0029762 |
0.02415 |
0.5448709 |
2.773912 |
0 |
189 |
up |
| DAUER_STAT3_TARGETS_UP |
0.0024570 |
0.02415 |
0.7096314 |
2.772893 |
0 |
46 |
up |
| AMIT_SERUM_RESPONSE_60_MCF10A |
0.0024570 |
0.02415 |
0.6770909 |
2.766897 |
0 |
55 |
up |
| ONDER_CDH1_TARGETS_1_DN |
0.0028986 |
0.02415 |
0.5501922 |
2.738067 |
0 |
159 |
up |
| REACTOME_NONSENSE_MEDIATED_DECAY_NMD |
0.0027701 |
0.02415 |
0.5907164 |
2.736406 |
0 |
108 |
up |
| IKEDA_MIR30_TARGETS_UP |
0.0027473 |
0.02415 |
0.5828889 |
2.736272 |
0 |
113 |
up |
| FLOTHO_PEDIATRIC_ALL_THERAPY_RESPONSE_UP |
0.0024450 |
0.02415 |
0.6804240 |
2.718141 |
0 |
49 |
up |
| GROSS_HYPOXIA_VIA_ELK3_DN |
0.0028011 |
0.02415 |
0.5572989 |
2.716872 |
0 |
145 |
up |
| GHANDHI_DIRECT_IRRADIATION_UP |
0.0026455 |
0.02415 |
0.5946343 |
2.689855 |
0 |
94 |
up |
| SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_UP |
0.0026667 |
0.02415 |
0.6159585 |
2.686289 |
0 |
80 |
up |
| CROONQUIST_STROMAL_STIMULATION_UP |
0.0024390 |
0.02415 |
0.6569458 |
2.680291 |
0 |
54 |
up |
| BURTON_ADIPOGENESIS_PEAK_AT_2HR |
0.0023923 |
0.02415 |
0.6918064 |
2.679870 |
0 |
43 |
up |
fgp <- fgsea_plot(fgsea_res$res_c3, pathways_title='C3 regulatory target genes', condition_name='PTGS2 low vs high')

kable(fgp)
| MIR3973 |
0.0030864 |
0.0090641 |
0.5470727 |
2.894165 |
0 |
244 |
up |
| MIR3617_5P |
0.0030769 |
0.0090641 |
0.5445195 |
2.875309 |
0 |
240 |
up |
| MIR641 |
0.0030769 |
0.0090641 |
0.5410508 |
2.858447 |
0 |
239 |
up |
| MIR4263 |
0.0030769 |
0.0090641 |
0.5282944 |
2.791053 |
0 |
239 |
up |
| MIR7844_5P |
0.0027933 |
0.0090641 |
0.5715168 |
2.777362 |
0 |
141 |
up |
| MIR195_3P |
0.0030120 |
0.0090641 |
0.5332156 |
2.762839 |
0 |
214 |
up |
| TAATGTG_MIR323 |
0.0027701 |
0.0090641 |
0.5567339 |
2.753735 |
0 |
152 |
up |
| MIR16_2_3P |
0.0030211 |
0.0090641 |
0.5286843 |
2.738449 |
0 |
213 |
up |
| CTTGTAT_MIR381 |
0.0029674 |
0.0090641 |
0.5421413 |
2.737655 |
0 |
187 |
up |
| MIR372_5P |
0.0030030 |
0.0090641 |
0.5179592 |
2.727421 |
0 |
230 |
up |
| ATTACAT_MIR3803P |
0.0026596 |
0.0090641 |
0.5935977 |
2.724402 |
0 |
96 |
up |
| ATGTTAA_MIR302C |
0.0030211 |
0.0090641 |
0.5165642 |
2.720880 |
0 |
231 |
up |
| ACTGAAA_MIR30A3P_MIR30E3P |
0.0029070 |
0.0090641 |
0.5345510 |
2.716809 |
0 |
190 |
up |
| MIR888_5P |
0.0030395 |
0.0090641 |
0.5198984 |
2.710661 |
0 |
222 |
up |
| MIR518A_5P_MIR527 |
0.0030960 |
0.0090641 |
0.5061683 |
2.671937 |
0 |
242 |
up |
| MIR34C_3P |
0.0025840 |
0.0090641 |
0.6273882 |
2.645229 |
0 |
62 |
up |
| MIR7853_5P |
0.0030488 |
0.0090641 |
0.5118496 |
2.627285 |
0 |
206 |
up |
| GTTATAT_MIR410 |
0.0025641 |
0.0090641 |
0.5781871 |
2.627247 |
0 |
85 |
up |
| MIR105_5P |
0.0030395 |
0.0090641 |
0.5112303 |
2.620522 |
0 |
205 |
up |
| MIR4760_5P |
0.0028986 |
0.0090641 |
0.5190253 |
2.617674 |
0 |
179 |
up |
| MIR148B_5P |
0.0025907 |
0.0090641 |
0.5937454 |
2.617599 |
0 |
73 |
up |
| MIR586 |
0.0031250 |
0.0090641 |
0.4926144 |
2.614530 |
0 |
258 |
up |
| MIR4477B |
0.0031646 |
0.0090641 |
0.4921498 |
2.603520 |
0 |
247 |
up |
| MIR3168 |
0.0027100 |
0.0090641 |
0.5398995 |
2.594522 |
0 |
126 |
up |
| MIR4735_5P |
0.0028736 |
0.0090641 |
0.5164255 |
2.593867 |
0 |
174 |
up |
| MIR548AV_3P |
0.0027855 |
0.0090641 |
0.5158359 |
2.592748 |
0 |
168 |
up |
| MIR4680_3P |
0.0030769 |
0.0090641 |
0.4906299 |
2.592066 |
0 |
239 |
up |
| GCATTTG_MIR105 |
0.0027322 |
0.0090641 |
0.5175262 |
2.590928 |
0 |
160 |
up |
| MIR8084 |
0.0030211 |
0.0090641 |
0.4922045 |
2.584189 |
0 |
227 |
up |
| MIR208A_5P |
0.0030769 |
0.0090641 |
0.4902642 |
2.583029 |
0 |
232 |
up |
fgp <- fgsea_plot(fgsea_res$res_c4, pathways_title='C4 cancer', condition_name='PTGS2 low vs high')

kable(fgp)
| GNF2_PTX3 |
0.0024752 |
0.014824 |
0.7760591 |
2.939477 |
0 |
35 |
up |
| GNF2_MMP1 |
0.0025445 |
0.014824 |
0.7942854 |
2.925008 |
0 |
31 |
up |
| GNF2_ST13 |
0.0025641 |
0.014824 |
0.6885203 |
2.882891 |
0 |
58 |
up |
| GNF2_DAP3 |
0.0028736 |
0.014824 |
0.5988357 |
2.881532 |
0 |
110 |
up |
| GNF2_EIF3S6 |
0.0028736 |
0.014824 |
0.5983728 |
2.879305 |
0 |
110 |
up |
| GNF2_RBBP6 |
0.0026525 |
0.014824 |
0.6455645 |
2.797187 |
0 |
68 |
up |
| MORF_TPT1 |
0.0028169 |
0.014824 |
0.5823326 |
2.715057 |
0 |
92 |
up |
| GNF2_TPT1 |
0.0024814 |
0.014824 |
0.7123200 |
2.709693 |
0 |
36 |
up |
| GCM_TPT1 |
0.0026110 |
0.014824 |
0.6309535 |
2.639473 |
0 |
59 |
up |
| MODULE_239 |
0.0029326 |
0.014824 |
0.5363332 |
2.583740 |
0 |
111 |
up |
| GNF2_CDH11 |
0.0024510 |
0.014824 |
0.7201195 |
2.529119 |
0 |
25 |
up |
| GNF2_FBL |
0.0030211 |
0.014824 |
0.5094511 |
2.522910 |
0 |
133 |
up |
| MORF_ACTG1 |
0.0030030 |
0.014824 |
0.5093717 |
2.505427 |
0 |
127 |
up |
| GCM_CSNK1A1 |
0.0025316 |
0.014824 |
0.6637386 |
2.492202 |
0 |
34 |
up |
| GNF2_CDC20 |
0.0016447 |
0.014824 |
-0.6465991 |
-2.485075 |
0 |
53 |
down |
| GNF2_PPP6C |
0.0024752 |
0.014824 |
0.6556029 |
2.483226 |
0 |
35 |
up |
| GNF2_PCNA |
0.0016026 |
0.014824 |
-0.6142481 |
-2.479466 |
0 |
65 |
down |
| GNF2_CCNB2 |
0.0016502 |
0.014824 |
-0.6396793 |
-2.465364 |
0 |
54 |
down |
| MODULE_332 |
0.0024752 |
0.014824 |
0.6176494 |
2.464857 |
0 |
44 |
up |
| GNF2_CCNA2 |
0.0016026 |
0.014824 |
-0.6099155 |
-2.461977 |
0 |
65 |
down |
| MODULE_29 |
0.0024814 |
0.014824 |
0.6916385 |
2.461552 |
0 |
26 |
up |
| MORF_JUND |
0.0025907 |
0.014824 |
0.5938818 |
2.448004 |
0 |
55 |
up |
| GNF2_TST |
0.0015504 |
0.014824 |
-0.5710539 |
-2.447333 |
0 |
95 |
down |
| GCM_ZNF198 |
0.0029326 |
0.014824 |
0.5077790 |
2.446182 |
0 |
111 |
up |
| GNF2_GSTM1 |
0.0015385 |
0.014824 |
-0.5600549 |
-2.433628 |
0 |
101 |
down |
| GNF2_ESPL1 |
0.0016722 |
0.014824 |
-0.6894501 |
-2.420771 |
0 |
35 |
down |
| GCM_NPM1 |
0.0029155 |
0.014824 |
0.5074841 |
2.413133 |
0 |
104 |
up |
| MORF_NPM1 |
0.0030211 |
0.014824 |
0.4752601 |
2.402117 |
0 |
149 |
up |
| GNF2_HMMR |
0.0016611 |
0.014824 |
-0.6321739 |
-2.365421 |
0 |
46 |
down |
| GNF2_RRM2 |
0.0016949 |
0.014824 |
-0.6586575 |
-2.364173 |
0 |
39 |
down |
fgp <- fgsea_plot(fgsea_res$res_c5, pathways_title='C5 GO genes', condition_name='PTGS2 low vs high')

kable(fgp)
fgp <- fgsea_plot(fgsea_res$res_c6, pathways_title='C6 oncogenic', condition_name='PTGS2 low vs high')

kable(fgp)
| STK33_NOMO_UP |
0.0031847 |
0.0118007 |
0.5656353 |
3.030833 |
0 |
267 |
up |
| STK33_UP |
0.0032468 |
0.0118007 |
0.5542519 |
2.969408 |
0 |
263 |
up |
| PIGF_UP.V1_UP |
0.0029412 |
0.0118007 |
0.5753524 |
2.928937 |
0 |
181 |
up |
| EGFR_UP.V1_UP |
0.0030120 |
0.0118007 |
0.5494265 |
2.783293 |
0 |
180 |
up |
| STK33_SKM_UP |
0.0031546 |
0.0118007 |
0.5161670 |
2.734754 |
0 |
246 |
up |
| VEGF_A_UP.V1_DN |
0.0029155 |
0.0118007 |
0.5179745 |
2.649386 |
0 |
184 |
up |
| CSR_EARLY_UP.V1_UP |
0.0027248 |
0.0118007 |
0.5059503 |
2.460275 |
0 |
139 |
up |
| HINATA_NFKB_IMMU_INF |
0.0022624 |
0.0118007 |
0.8305516 |
2.411343 |
0 |
14 |
up |
| HOXA9_DN.V1_UP |
0.0029499 |
0.0118007 |
0.4711044 |
2.375012 |
0 |
170 |
up |
| TBK1.DF_DN |
0.0032154 |
0.0118007 |
0.4256881 |
2.280401 |
0 |
265 |
up |
| BMI1_DN_MEL18_DN.V1_UP |
0.0027027 |
0.0118007 |
0.4664368 |
2.269241 |
0 |
135 |
up |
| SIRNA_EIF4GI_DN |
0.0025063 |
0.0118007 |
0.4922075 |
2.254878 |
0 |
88 |
up |
| TBK1.DF_UP |
0.0032468 |
0.0118007 |
0.4069310 |
2.180135 |
0 |
263 |
up |
| PRC2_EED_UP.V1_DN |
0.0015152 |
0.0118007 |
-0.4511859 |
-2.151955 |
0 |
179 |
down |
| PDGF_UP.V1_UP |
0.0026738 |
0.0118007 |
0.4345148 |
2.109846 |
0 |
133 |
up |
| ATF2_UP.V1_DN |
0.0030120 |
0.0118007 |
0.4173613 |
2.103911 |
0 |
171 |
up |
| TGFB_UP.V1_UP |
0.0029674 |
0.0118007 |
0.4141101 |
2.097955 |
0 |
176 |
up |
| BCAT_BILD_ET_AL_DN |
0.0023981 |
0.0118007 |
0.5238755 |
2.095760 |
0 |
45 |
up |
| CAMP_UP.V1_DN |
0.0029326 |
0.0118007 |
0.4011555 |
2.054361 |
0 |
186 |
up |
| RPS14_DN.V1_UP |
0.0029240 |
0.0118007 |
0.4017856 |
2.052952 |
0 |
182 |
up |
| KRAS.50_UP.V1_UP |
0.0023981 |
0.0118007 |
0.5052717 |
2.021336 |
0 |
45 |
up |
| SRC_UP.V1_UP |
0.0015898 |
0.0118007 |
-0.4361672 |
-2.011706 |
0 |
148 |
down |
| ERBB2_UP.V1_DN |
0.0029240 |
0.0118007 |
0.3924639 |
2.005323 |
0 |
182 |
up |
| KRAS.600_UP.V1_UP |
0.0032362 |
0.0118007 |
0.3776060 |
1.994830 |
0 |
244 |
up |
| E2F1_UP.V1_DN |
0.0029674 |
0.0118007 |
0.3929226 |
1.990615 |
0 |
176 |
up |
| EIF4E_DN |
0.0025189 |
0.0118007 |
0.4228544 |
1.954819 |
0 |
94 |
up |
| RAF_UP.V1_UP |
0.0029240 |
0.0118007 |
0.3845223 |
1.952555 |
0 |
179 |
up |
| KRAS.KIDNEY_UP.V1_UP |
0.0026525 |
0.0118007 |
0.3983047 |
1.931468 |
0 |
130 |
up |
| BMI1_DN.V1_UP |
0.0026738 |
0.0118007 |
0.3974161 |
1.929709 |
0 |
133 |
up |
| LTE2_UP.V1_DN |
0.0029240 |
0.0118007 |
0.3775259 |
1.928996 |
0 |
182 |
up |
fgp <- fgsea_plot(fgsea_res$res_c7, pathways_title='C7 immunologic', condition_name='PTGS2 low vs high')

kable(fgp)
| GSE9988_LOW_LPS_VS_CTRL_TREATED_MONOCYTE_UP |
0.0028249 |
0.0111171 |
0.6626050 |
3.414764 |
0 |
178 |
up |
| GSE9988_LOW_LPS_VS_VEHICLE_TREATED_MONOCYTE_UP |
0.0028736 |
0.0111171 |
0.6476534 |
3.319183 |
0 |
175 |
up |
| GSE14769_UNSTIM_VS_80MIN_LPS_BMDM_DN |
0.0030395 |
0.0111171 |
0.6270112 |
3.249431 |
0 |
191 |
up |
| GSE9988_LPS_VS_CTRL_TREATED_MONOCYTE_UP |
0.0028736 |
0.0111171 |
0.6315690 |
3.236751 |
0 |
175 |
up |
| GSE9988_LPS_VS_VEHICLE_TREATED_MONOCYTE_UP |
0.0028490 |
0.0111171 |
0.6278268 |
3.223876 |
0 |
176 |
up |
| GSE14769_UNSTIM_VS_60MIN_LPS_BMDM_DN |
0.0031056 |
0.0111171 |
0.6206065 |
3.210482 |
0 |
192 |
up |
| GSE30971_CTRL_VS_LPS_STIM_MACROPHAGE_WBP7_KO_4H_UP |
0.0029155 |
0.0111171 |
0.6155783 |
3.181285 |
0 |
181 |
up |
| GSE29617_CTRL_VS_DAY7_TIV_FLU_VACCINE_PBMC_2008_UP |
0.0028653 |
0.0111171 |
0.6123084 |
3.169453 |
0 |
180 |
up |
| GSE30971_CTRL_VS_LPS_STIM_MACROPHAGE_WBP7_KO_2H_UP |
0.0028490 |
0.0111171 |
0.6108320 |
3.152408 |
0 |
179 |
up |
| GSE9988_ANTI_TREM1_VS_ANTI_TREM1_AND_LPS_MONOCYTE_DN |
0.0029240 |
0.0111171 |
0.6165688 |
3.143318 |
0 |
172 |
up |
| GSE21678_WT_VS_FOXO1_FOXO3_KO_TREG_UP |
0.0028736 |
0.0111171 |
0.6032215 |
3.091472 |
0 |
175 |
up |
| GSE42021_TREG_PLN_VS_CD24INT_TREG_THYMUS_UP |
0.0030211 |
0.0111171 |
0.5868058 |
3.046850 |
0 |
195 |
up |
| GSE9988_ANTI_TREM1_AND_LPS_VS_CTRL_TREATED_MONOCYTES_UP |
0.0028329 |
0.0111171 |
0.5888956 |
3.027887 |
0 |
177 |
up |
| GSE369_PRE_VS_POST_IL6_INJECTION_SOCS3_KO_LIVER_UP |
0.0028653 |
0.0111171 |
0.5848084 |
3.027107 |
0 |
180 |
up |
| GSE30971_CTRL_VS_LPS_STIM_MACROPHAGE_WBP7_HET_2H_UP |
0.0028490 |
0.0111171 |
0.5758679 |
2.971964 |
0 |
179 |
up |
| GSE12392_IFNAR_KO_VS_IFNB_KO_CD8_NEG_SPLEEN_DC_UP |
0.0029070 |
0.0111171 |
0.5690880 |
2.945833 |
0 |
184 |
up |
| GSE27434_WT_VS_DNMT1_KO_TREG_DN |
0.0030864 |
0.0111171 |
0.5675373 |
2.944801 |
0 |
193 |
up |
| GSE9988_ANTI_TREM1_VS_CTRL_TREATED_MONOCYTES_UP |
0.0028490 |
0.0111171 |
0.5681529 |
2.942839 |
0 |
183 |
up |
| GSE30971_WBP7_HET_VS_KO_MACROPHAGE_2H_LPS_STIM_DN |
0.0030960 |
0.0111171 |
0.5680119 |
2.930968 |
0 |
189 |
up |
| GSE9988_ANTI_TREM1_VS_VEHICLE_TREATED_MONOCYTES_UP |
0.0028490 |
0.0111171 |
0.5663335 |
2.908109 |
0 |
176 |
up |
| GSE29617_CTRL_VS_TIV_FLU_VACCINE_PBMC_2008_UP |
0.0029326 |
0.0111171 |
0.5708043 |
2.901657 |
0 |
171 |
up |
| GSE14769_UNSTIM_VS_40MIN_LPS_BMDM_DN |
0.0030488 |
0.0111171 |
0.5583699 |
2.899976 |
0 |
194 |
up |
| GSE9988_ANTI_TREM1_VS_LOW_LPS_MONOCYTE_DN |
0.0028902 |
0.0111171 |
0.5565787 |
2.881626 |
0 |
182 |
up |
| GSE2706_UNSTIM_VS_2H_LPS_DC_DN |
0.0028490 |
0.0111171 |
0.5568357 |
2.859338 |
0 |
176 |
up |
| GSE14769_UNSTIM_VS_120MIN_LPS_BMDM_DN |
0.0030769 |
0.0111171 |
0.5487134 |
2.850829 |
0 |
197 |
up |
| GSE9988_ANTI_TREM1_VS_LPS_MONOCYTE_DN |
0.0028902 |
0.0111171 |
0.5473705 |
2.833952 |
0 |
182 |
up |
| GSE45365_NK_CELL_VS_CD11B_DC_DN |
0.0030488 |
0.0111171 |
0.5440801 |
2.825760 |
0 |
194 |
up |
| GSE37605_FOXP3_FUSION_GFP_VS_IRES_GFP_TREG_C57BL6_DN |
0.0029155 |
0.0111171 |
0.5543919 |
2.808944 |
0 |
166 |
up |
| GSE1791_CTRL_VS_NEUROMEDINU_IN_T_CELL_LINE_6H_UP |
0.0030488 |
0.0111171 |
0.5434117 |
2.798492 |
0 |
187 |
up |
| GSE42021_TCONV_PLN_VS_TREG_PRECURSORS_THYMUS_DN |
0.0029940 |
0.0111171 |
0.5330160 |
2.777363 |
0 |
196 |
up |
fgp <- fgsea_plot(fgsea_res$res_msg, pathways_title='All signatures', condition_name='PTGS2 low vs high')

kable(fgp)
| HALLMARK_TNFA_SIGNALING_VIA_NFKB |
0.0028653 |
0.0162184 |
0.6718790 |
3.481502 |
0 |
195 |
up |
| GSE9988_LOW_LPS_VS_CTRL_TREATED_MONOCYTE_UP |
0.0028490 |
0.0162184 |
0.6626050 |
3.390014 |
0 |
178 |
up |
| GSE9988_LOW_LPS_VS_VEHICLE_TREATED_MONOCYTE_UP |
0.0028490 |
0.0162184 |
0.6476534 |
3.294299 |
0 |
175 |
up |
| GSE14769_UNSTIM_VS_80MIN_LPS_BMDM_DN |
0.0028986 |
0.0162184 |
0.6270112 |
3.241875 |
0 |
191 |
up |
| GSE9988_LPS_VS_CTRL_TREATED_MONOCYTE_UP |
0.0028490 |
0.0162184 |
0.6315690 |
3.212485 |
0 |
175 |
up |
| GSE14769_UNSTIM_VS_60MIN_LPS_BMDM_DN |
0.0028736 |
0.0162184 |
0.6206065 |
3.212151 |
0 |
192 |
up |
| GSE9988_LPS_VS_VEHICLE_TREATED_MONOCYTE_UP |
0.0028409 |
0.0162184 |
0.6278268 |
3.201612 |
0 |
176 |
up |
| PHONG_TNF_TARGETS_UP |
0.0025253 |
0.0162184 |
0.7491497 |
3.164731 |
0 |
62 |
up |
| GSE30971_CTRL_VS_LPS_STIM_MACROPHAGE_WBP7_KO_4H_UP |
0.0028653 |
0.0162184 |
0.6155783 |
3.161371 |
0 |
181 |
up |
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION |
0.0027933 |
0.0162184 |
0.6070484 |
3.151892 |
0 |
189 |
up |
| GSE29617_CTRL_VS_DAY7_TIV_FLU_VACCINE_PBMC_2008_UP |
0.0028818 |
0.0162184 |
0.6123084 |
3.134740 |
0 |
180 |
up |
| GSE9988_ANTI_TREM1_VS_ANTI_TREM1_AND_LPS_MONOCYTE_DN |
0.0027933 |
0.0162184 |
0.6165688 |
3.134079 |
0 |
172 |
up |
| GSE30971_CTRL_VS_LPS_STIM_MACROPHAGE_WBP7_KO_2H_UP |
0.0028653 |
0.0162184 |
0.6108320 |
3.133882 |
0 |
179 |
up |
| CHEN_HOXA5_TARGETS_9HR_UP |
0.0029499 |
0.0162184 |
0.5944775 |
3.128150 |
0 |
211 |
up |
| ANASTASSIOU_MULTICANCER_INVASIVENESS_SIGNATURE |
0.0025253 |
0.0162184 |
0.7340077 |
3.100765 |
0 |
62 |
up |
| GSE21678_WT_VS_FOXO1_FOXO3_KO_TREG_UP |
0.0028490 |
0.0162184 |
0.6032215 |
3.068295 |
0 |
175 |
up |
| ZWANG_CLASS_3_TRANSIENTLY_INDUCED_BY_EGF |
0.0029851 |
0.0162184 |
0.5855923 |
3.066533 |
0 |
219 |
up |
| PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_DN |
0.0027473 |
0.0162184 |
0.6237117 |
3.056225 |
0 |
128 |
up |
| BROCKE_APOPTOSIS_REVERSED_BY_IL6 |
0.0027322 |
0.0162184 |
0.6128985 |
3.051603 |
0 |
140 |
up |
| STK33_NOMO_UP |
0.0030303 |
0.0162184 |
0.5656353 |
3.044058 |
0 |
267 |
up |
| GSE42021_TREG_PLN_VS_CD24INT_TREG_THYMUS_UP |
0.0028653 |
0.0162184 |
0.5868058 |
3.040675 |
0 |
195 |
up |
| MODULE_47 |
0.0029762 |
0.0162184 |
0.5783163 |
3.039443 |
0 |
214 |
up |
| GABRIELY_MIR21_TARGETS |
0.0030864 |
0.0162184 |
0.5621520 |
3.019703 |
0 |
271 |
up |
| GO_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE |
0.0025253 |
0.0162184 |
0.6543159 |
3.016019 |
0 |
94 |
up |
| GSE9988_ANTI_TREM1_AND_LPS_VS_CTRL_TREATED_MONOCYTES_UP |
0.0028653 |
0.0162184 |
0.5888956 |
2.996015 |
0 |
177 |
up |
| GSE369_PRE_VS_POST_IL6_INJECTION_SOCS3_KO_LIVER_UP |
0.0028818 |
0.0162184 |
0.5848084 |
2.993953 |
0 |
180 |
up |
| KEGG_RIBOSOME |
0.0025189 |
0.0162184 |
0.6687799 |
2.991657 |
0 |
81 |
up |
| TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_UP |
0.0025000 |
0.0162184 |
0.6959614 |
2.985121 |
0 |
66 |
up |
| STK33_UP |
0.0030030 |
0.0162184 |
0.5542519 |
2.980015 |
0 |
263 |
up |
| UZONYI_RESPONSE_TO_LEUKOTRIENE_AND_THROMBIN |
0.0023981 |
0.0162184 |
0.8018658 |
2.965318 |
0 |
34 |
up |